Inferential Structure Determination of Chromosomes from Single-Cell Hi-C Data

Topology, structures, and energy landscapes of human chromosomes

(2015) Bin Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Manifold Based Optimization for Single-Cell 3D Genome Reconstruction

(2015) Jonas Paulsen et al.   PLoS Computational Biology

A statistical approach for inferring the 3D structure of the genome

(2014) N. Varoquaux et al.   BIOINFORMATICS

Predictive Polymer Modeling Reveals Coupled Fluctuations in Chromosome Conformation and Transcription

(2014) Luca Giorgetti et al.   CELL

3D genome reconstruction from chromosomal contacts

(2014) Annick Lesne et al.   NATURE METHODS

Large-scale reconstruction of 3D structures of human chromosomes from chromosomal contact data

(2014) Tuan Trieu et al.   NUCLEIC ACIDS RESEARCH

Mantel test in population genetics

(2013) José Alexandre F. Diniz-Filho et al.   GENETICS AND MOLECULAR BIOLOGY

3D Chromosome Modeling with Semi-Definite Programming and Hi-C Data

(2013) ZhiZhuo Zhang et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

(2013) Takashi Nagano et al.   NATURE

Dismantling the Mantel tests

(2013) Gilles Guillot et al.   Methods in Ecology and Evolution

Bayesian Inference of Spatial Organizations of Chromosomes

(2013) Ming Hu et al.   PLoS Computational Biology

The statistical-mechanics of chromosome conformation capture

(2013) Justin M O'Sullivan et al.   Nucleus

CSB: a Python framework for structural bioinformatics

(2012) I. Kalev et al.   BIOINFORMATICS

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Recovering ensembles of chromatin conformations from contact probabilities

(2012) Dario Meluzzi et al.   NUCLEIC ACIDS RESEARCH

Complexity of chromatin folding is captured by the strings and binders switch model

(2012) M. Barbieri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies

(2012) Daniel Russel et al.   PLOS BIOLOGY

Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling

(2011) Mathieu Rousseau et al.   BMC BIOINFORMATICS

The fractal globule as a model of chromatin architecture in the cell

(2011) Leonid A. Mirny   CHROMOSOME RESEARCH

Genome architectures revealed by tethered chromosome conformation capture and population-based modeling

(2011) Reza Kalhor et al.   NATURE BIOTECHNOLOGY

Statistical mechanics analysis of sparse data

(2010) Michael Habeck   JOURNAL OF STRUCTURAL BIOLOGY

A three-dimensional model of the yeast genome

(2010) Zhijun Duan et al.   NATURE

The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules

(2010) Davide Baù et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Chromosome Territories

(2010) T. Cremer et al.   Cold Spring Harbor Perspectives in Biology

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

ISD: a software package for Bayesian NMR structure calculation

(2008) W. Rieping et al.   BIOINFORMATICS

Eukaryotic gene regulation in three dimensions and its impact on genome evolution

(2008) M Madan Babu et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Structure and Dynamics of Interphase Chromosomes

(2008) Angelo Rosa et al.   PLoS Computational Biology